Variant report

Variant	rs1123390
Chromosome Location	chr5:1976500-1976501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1970121..1972284-chr5:1974533..1976693,2	K562	blood:
2	chr5:1975910..1976629-chr5:2038577..2039238,2	MCF-7	breast:
3	chr5:1976228..1977009-chr5:2038725..2039367,2	MCF-7	breast:
4	chr5:1800213..1802017-chr5:1975068..1977330,2	MCF-7	breast:
5	chr5:1797328..1800082-chr5:1975241..1976881,2	MCF-7	breast:
6	chr5:1976483..1978834-chr5:2046754..2049581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10035144	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041900	0.82[CEU][hapmap]
rs10043083	0.92[ASN][1000 genomes]
rs10045683	0.99[ASN][1000 genomes]
rs10053882	0.83[CHB][hapmap]
rs1017924	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1023980	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1023981	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[EUR][1000 genomes]
rs10474733	0.85[ASN][1000 genomes]
rs10474734	0.85[ASN][1000 genomes]
rs10475126	0.81[EUR][1000 genomes]
rs10475128	0.81[EUR][1000 genomes]
rs11133918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11133920	0.81[EUR][1000 genomes]
rs1123381	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749073	0.85[ASN][1000 genomes]
rs11952205	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188545	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12654102	0.82[ASN][1000 genomes]
rs12716127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13166888	0.99[ASN][1000 genomes]
rs1486937	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1601641	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3902820	0.92[ASN][1000 genomes]
rs4246752	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4263538	0.80[EUR][1000 genomes]
rs4371796	0.99[ASN][1000 genomes]
rs4398680	0.81[ASN][1000 genomes]
rs4407661	0.99[ASN][1000 genomes]
rs4526149	0.92[ASN][1000 genomes]
rs4975775	0.90[GIH][hapmap]
rs4975777	0.99[ASN][1000 genomes]
rs4975779	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975786	0.85[ASN][1000 genomes]
rs55860207	0.86[ASN][1000 genomes]
rs57434783	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61656301	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62337135	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67659713	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6870127	0.81[EUR][1000 genomes]
rs9312970	0.85[ASN][1000 genomes]
rs965276	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1123390	SLC9A3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1974800-1977200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr5:1974800-1977400	Enhancers	Dnd41	blood
3	chr5:1975600-1976600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:1976200-1976800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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